Starting phenix.real_space_refine on Tue Jul 29 02:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.map" model { file = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2025/8iov_35626.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4220 2.51 5 N 1075 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6607 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.42, per 1000 atoms: 0.82 Number of scatterers: 6607 At special positions: 0 Unit cell: (98.49, 72.36, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1275 8.00 N 1075 7.00 C 4220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 55.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.529A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.983A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.781A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.996A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.878A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.762A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.693A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.040A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.675A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.286A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.507A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.890A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.554A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.707A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.056A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.028A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.781A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2080 1.34 - 1.46: 1702 1.46 - 1.58: 2951 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6791 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 9044 1.95 - 3.90: 150 3.90 - 5.85: 30 5.85 - 7.80: 6 7.80 - 9.76: 2 Bond angle restraints: 9232 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" C ASN A 432 " pdb=" CA ASN A 432 " pdb=" CB ASN A 432 " ideal model delta sigma weight residual 110.84 106.14 4.70 1.66e+00 3.63e-01 8.01e+00 angle pdb=" CB MET A 190 " pdb=" CG MET A 190 " pdb=" SD MET A 190 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N GLU A 75 " pdb=" CA GLU A 75 " pdb=" CB GLU A 75 " ideal model delta sigma weight residual 110.16 114.01 -3.85 1.48e+00 4.57e-01 6.77e+00 angle pdb=" C ASP A 431 " pdb=" N ASN A 432 " pdb=" CA ASN A 432 " ideal model delta sigma weight residual 121.19 124.95 -3.76 1.59e+00 3.96e-01 5.59e+00 ... (remaining 9227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3981 21.98 - 43.96: 180 43.96 - 65.94: 14 65.94 - 87.92: 17 87.92 - 109.90: 8 Dihedral angle restraints: 4200 sinusoidal: 1876 harmonic: 2324 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -2.91 -83.09 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N GLU A 433 " pdb=" CA GLU A 433 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1006 0.230 - 0.459: 4 0.459 - 0.689: 1 0.689 - 0.919: 0 0.919 - 1.148: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 1009 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" CG ASN A 103 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.017 2.00e-02 2.50e+03 1.67e-02 3.50e+00 pdb=" CG ASN A 432 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 610 " 0.011 2.00e-02 2.50e+03 1.09e-02 2.95e+00 pdb=" CG TRP A 610 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 610 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 610 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 610 " -0.000 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1075 2.76 - 3.29: 6290 3.29 - 3.83: 10695 3.83 - 4.36: 12048 4.36 - 4.90: 21060 Nonbonded interactions: 51168 Sorted by model distance: nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.222 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.242 3.040 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.293 3.120 nonbonded pdb=" O ALA B 344 " pdb=" OG1 THR B 345 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.309 3.040 ... (remaining 51163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6813 Z= 0.160 Angle : 0.677 12.215 9291 Z= 0.311 Chirality : 0.060 1.148 1012 Planarity : 0.003 0.041 1173 Dihedral : 13.944 109.902 2687 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 787 helix: 1.92 (0.26), residues: 397 sheet: 2.72 (0.76), residues: 42 loop : -0.63 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 32 TYR 0.014 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 7) link_NAG-ASN : angle 5.15973 ( 21) link_ALPHA1-6 : bond 0.00387 ( 1) link_ALPHA1-6 : angle 1.51806 ( 3) link_BETA1-4 : bond 0.00458 ( 6) link_BETA1-4 : angle 2.05393 ( 18) link_ALPHA1-3 : bond 0.00264 ( 1) link_ALPHA1-3 : angle 1.59110 ( 3) hydrogen bonds : bond 0.12130 ( 308) hydrogen bonds : angle 5.04275 ( 873) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.83345 ( 14) covalent geometry : bond 0.00313 ( 6791) covalent geometry : angle 0.62121 ( 9232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1881 time to fit residues: 15.1898 Evaluate side-chains 43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 70 optimal weight: 0.0770 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058365 restraints weight = 20543.871| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.87 r_work: 0.2900 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6813 Z= 0.111 Angle : 0.597 10.012 9291 Z= 0.284 Chirality : 0.046 0.371 1012 Planarity : 0.003 0.036 1173 Dihedral : 9.766 65.093 1165 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.58 % Allowed : 4.61 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 787 helix: 2.01 (0.26), residues: 394 sheet: 2.12 (0.73), residues: 42 loop : -0.62 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 535 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 7) link_NAG-ASN : angle 3.71788 ( 21) link_ALPHA1-6 : bond 0.00634 ( 1) link_ALPHA1-6 : angle 1.71603 ( 3) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 2.25959 ( 18) link_ALPHA1-3 : bond 0.00846 ( 1) link_ALPHA1-3 : angle 2.29084 ( 3) hydrogen bonds : bond 0.04417 ( 308) hydrogen bonds : angle 4.44704 ( 873) SS BOND : bond 0.00151 ( 7) SS BOND : angle 1.47008 ( 14) covalent geometry : bond 0.00229 ( 6791) covalent geometry : angle 0.55768 ( 9232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1973 time to fit residues: 13.8308 Evaluate side-chains 45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055144 restraints weight = 21042.140| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.95 r_work: 0.2765 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6813 Z= 0.167 Angle : 0.610 10.260 9291 Z= 0.295 Chirality : 0.046 0.356 1012 Planarity : 0.003 0.033 1173 Dihedral : 7.526 56.635 1165 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.72 % Allowed : 6.20 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 787 helix: 2.01 (0.26), residues: 394 sheet: 1.74 (0.78), residues: 44 loop : -0.64 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 610 HIS 0.005 0.001 HIS A 401 PHE 0.015 0.001 PHE B 347 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 7) link_NAG-ASN : angle 3.64911 ( 21) link_ALPHA1-6 : bond 0.01019 ( 1) link_ALPHA1-6 : angle 2.58201 ( 3) link_BETA1-4 : bond 0.00425 ( 6) link_BETA1-4 : angle 2.20206 ( 18) link_ALPHA1-3 : bond 0.00808 ( 1) link_ALPHA1-3 : angle 2.27754 ( 3) hydrogen bonds : bond 0.05212 ( 308) hydrogen bonds : angle 4.49783 ( 873) SS BOND : bond 0.00163 ( 7) SS BOND : angle 1.86944 ( 14) covalent geometry : bond 0.00376 ( 6791) covalent geometry : angle 0.57050 ( 9232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.1878 time to fit residues: 12.0587 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.054007 restraints weight = 21393.290| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.95 r_work: 0.2731 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6813 Z= 0.176 Angle : 0.607 10.261 9291 Z= 0.297 Chirality : 0.046 0.371 1012 Planarity : 0.003 0.032 1173 Dihedral : 6.255 50.999 1165 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 7.06 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.31), residues: 787 helix: 1.84 (0.26), residues: 400 sheet: 1.72 (0.82), residues: 43 loop : -0.70 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.005 0.001 HIS A 401 PHE 0.013 0.001 PHE B 347 TYR 0.012 0.001 TYR A 50 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 7) link_NAG-ASN : angle 3.75697 ( 21) link_ALPHA1-6 : bond 0.00405 ( 1) link_ALPHA1-6 : angle 1.66449 ( 3) link_BETA1-4 : bond 0.00374 ( 6) link_BETA1-4 : angle 2.01439 ( 18) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 2.29951 ( 3) hydrogen bonds : bond 0.05319 ( 308) hydrogen bonds : angle 4.53003 ( 873) SS BOND : bond 0.00163 ( 7) SS BOND : angle 1.99709 ( 14) covalent geometry : bond 0.00399 ( 6791) covalent geometry : angle 0.56752 ( 9232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8684 (mp0) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.1826 time to fit residues: 11.7316 Evaluate side-chains 46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.053675 restraints weight = 21047.351| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.93 r_work: 0.2724 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6813 Z= 0.176 Angle : 0.606 10.524 9291 Z= 0.297 Chirality : 0.045 0.370 1012 Planarity : 0.003 0.032 1173 Dihedral : 5.877 43.447 1165 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 7.93 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.31), residues: 787 helix: 1.86 (0.26), residues: 401 sheet: 1.22 (0.82), residues: 48 loop : -0.66 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.004 0.001 HIS A 34 PHE 0.011 0.001 PHE B 347 TYR 0.013 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 7) link_NAG-ASN : angle 3.76115 ( 21) link_ALPHA1-6 : bond 0.00569 ( 1) link_ALPHA1-6 : angle 1.77762 ( 3) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 1.95610 ( 18) link_ALPHA1-3 : bond 0.00891 ( 1) link_ALPHA1-3 : angle 1.90596 ( 3) hydrogen bonds : bond 0.05399 ( 308) hydrogen bonds : angle 4.54547 ( 873) SS BOND : bond 0.00143 ( 7) SS BOND : angle 2.03351 ( 14) covalent geometry : bond 0.00402 ( 6791) covalent geometry : angle 0.56738 ( 9232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8690 (mp0) outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 0.1912 time to fit residues: 12.1355 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054629 restraints weight = 20693.968| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.96 r_work: 0.2770 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6813 Z= 0.138 Angle : 0.582 10.287 9291 Z= 0.283 Chirality : 0.044 0.365 1012 Planarity : 0.003 0.034 1173 Dihedral : 5.353 34.723 1165 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 8.21 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 787 helix: 1.89 (0.26), residues: 402 sheet: 1.57 (0.81), residues: 43 loop : -0.64 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 7) link_NAG-ASN : angle 3.73453 ( 21) link_ALPHA1-6 : bond 0.00622 ( 1) link_ALPHA1-6 : angle 1.65889 ( 3) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 1.84361 ( 18) link_ALPHA1-3 : bond 0.00899 ( 1) link_ALPHA1-3 : angle 1.78068 ( 3) hydrogen bonds : bond 0.04989 ( 308) hydrogen bonds : angle 4.44667 ( 873) SS BOND : bond 0.00115 ( 7) SS BOND : angle 1.91772 ( 14) covalent geometry : bond 0.00308 ( 6791) covalent geometry : angle 0.54361 ( 9232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8595 (mt-10) REVERT: B 471 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8718 (mp0) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.3003 time to fit residues: 18.3536 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055721 restraints weight = 20690.867| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.97 r_work: 0.2801 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6813 Z= 0.111 Angle : 0.561 10.159 9291 Z= 0.269 Chirality : 0.043 0.353 1012 Planarity : 0.003 0.035 1173 Dihedral : 4.859 34.165 1165 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.43 % Allowed : 8.93 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.31), residues: 787 helix: 1.94 (0.26), residues: 401 sheet: 1.57 (0.80), residues: 43 loop : -0.55 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.008 0.001 PHE B 342 TYR 0.011 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 7) link_NAG-ASN : angle 3.66619 ( 21) link_ALPHA1-6 : bond 0.00811 ( 1) link_ALPHA1-6 : angle 1.67853 ( 3) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 1.76776 ( 18) link_ALPHA1-3 : bond 0.00851 ( 1) link_ALPHA1-3 : angle 1.59946 ( 3) hydrogen bonds : bond 0.04501 ( 308) hydrogen bonds : angle 4.32810 ( 873) SS BOND : bond 0.00105 ( 7) SS BOND : angle 1.77948 ( 14) covalent geometry : bond 0.00234 ( 6791) covalent geometry : angle 0.52277 ( 9232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.9599 (mmmm) cc_final: 0.9387 (mmmm) REVERT: B 406 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8691 (mt-10) REVERT: B 471 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8944 (mm-30) outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.1942 time to fit residues: 12.6209 Evaluate side-chains 45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055481 restraints weight = 21039.692| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.99 r_work: 0.2773 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6813 Z= 0.120 Angle : 0.567 10.220 9291 Z= 0.273 Chirality : 0.043 0.353 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.710 34.169 1165 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.43 % Allowed : 8.93 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 787 helix: 1.93 (0.26), residues: 402 sheet: 1.65 (0.80), residues: 43 loop : -0.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.008 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 7) link_NAG-ASN : angle 3.58305 ( 21) link_ALPHA1-6 : bond 0.00692 ( 1) link_ALPHA1-6 : angle 1.63531 ( 3) link_BETA1-4 : bond 0.00347 ( 6) link_BETA1-4 : angle 1.75852 ( 18) link_ALPHA1-3 : bond 0.00765 ( 1) link_ALPHA1-3 : angle 1.60866 ( 3) hydrogen bonds : bond 0.04589 ( 308) hydrogen bonds : angle 4.34845 ( 873) SS BOND : bond 0.00111 ( 7) SS BOND : angle 1.76657 ( 14) covalent geometry : bond 0.00263 ( 6791) covalent geometry : angle 0.53110 ( 9232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8764 (mmp) cc_final: 0.8558 (mmt) REVERT: B 406 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8642 (mt-10) REVERT: B 471 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8949 (mm-30) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1775 time to fit residues: 11.8466 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055182 restraints weight = 21067.927| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.96 r_work: 0.2767 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6813 Z= 0.131 Angle : 0.585 10.165 9291 Z= 0.281 Chirality : 0.043 0.355 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.635 33.564 1165 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.14 % Allowed : 9.22 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 787 helix: 1.95 (0.26), residues: 402 sheet: 1.65 (0.81), residues: 43 loop : -0.52 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 610 HIS 0.003 0.001 HIS A 34 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 3.57942 ( 21) link_ALPHA1-6 : bond 0.00712 ( 1) link_ALPHA1-6 : angle 1.65198 ( 3) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 1.75752 ( 18) link_ALPHA1-3 : bond 0.00713 ( 1) link_ALPHA1-3 : angle 1.57157 ( 3) hydrogen bonds : bond 0.04666 ( 308) hydrogen bonds : angle 4.35196 ( 873) SS BOND : bond 0.00121 ( 7) SS BOND : angle 1.79677 ( 14) covalent geometry : bond 0.00292 ( 6791) covalent geometry : angle 0.55036 ( 9232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 474 MET cc_start: 0.8744 (mmp) cc_final: 0.8541 (mmt) REVERT: B 471 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8947 (mm-30) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1838 time to fit residues: 12.1799 Evaluate side-chains 45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.5980 chunk 26 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054834 restraints weight = 21178.990| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.21 r_work: 0.2770 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6813 Z= 0.113 Angle : 0.583 10.544 9291 Z= 0.281 Chirality : 0.043 0.351 1012 Planarity : 0.003 0.035 1173 Dihedral : 4.507 33.265 1165 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.29 % Allowed : 9.80 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 787 helix: 1.97 (0.26), residues: 402 sheet: 1.67 (0.80), residues: 43 loop : -0.50 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.008 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 7) link_NAG-ASN : angle 3.51060 ( 21) link_ALPHA1-6 : bond 0.00791 ( 1) link_ALPHA1-6 : angle 1.63167 ( 3) link_BETA1-4 : bond 0.00374 ( 6) link_BETA1-4 : angle 1.70063 ( 18) link_ALPHA1-3 : bond 0.00752 ( 1) link_ALPHA1-3 : angle 1.51701 ( 3) hydrogen bonds : bond 0.04427 ( 308) hydrogen bonds : angle 4.32086 ( 873) SS BOND : bond 0.00101 ( 7) SS BOND : angle 1.71253 ( 14) covalent geometry : bond 0.00244 ( 6791) covalent geometry : angle 0.55002 ( 9232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8980 (mm-30) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1699 time to fit residues: 11.4508 Evaluate side-chains 46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053856 restraints weight = 21215.590| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.20 r_work: 0.2747 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6813 Z= 0.142 Angle : 0.589 10.152 9291 Z= 0.286 Chirality : 0.043 0.352 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.523 32.819 1165 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 787 helix: 1.96 (0.26), residues: 402 sheet: 1.62 (0.80), residues: 43 loop : -0.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 610 HIS 0.003 0.001 HIS A 34 PHE 0.008 0.001 PHE A 523 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 3.52423 ( 21) link_ALPHA1-6 : bond 0.00720 ( 1) link_ALPHA1-6 : angle 1.63174 ( 3) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.73009 ( 18) link_ALPHA1-3 : bond 0.00702 ( 1) link_ALPHA1-3 : angle 1.60577 ( 3) hydrogen bonds : bond 0.04721 ( 308) hydrogen bonds : angle 4.38378 ( 873) SS BOND : bond 0.00127 ( 7) SS BOND : angle 1.80188 ( 14) covalent geometry : bond 0.00321 ( 6791) covalent geometry : angle 0.55528 ( 9232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.17 seconds wall clock time: 70 minutes 29.55 seconds (4229.55 seconds total)